Last updated on 2024-11-08 07:50:53 CET.
| Package | ERROR | OK |
|---|---|---|
| AnnotationBustR | 13 | |
| dietr | 1 | 12 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 12
Version: 1.1.5-1
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/66s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> test_check("dietr")
Loading required package: dietr
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: rapi_execute(stmt, arrow, integer64)
2: withCallingHandlers(expr, condition = function(cnd) { { .__handler_frame__. <- TRUE .__setup_frame__. <- frame if (inherits(cnd, "message")) { except <- c("warning", "error") } else if (inherits(cnd, "warning")) { except <- "error" } else { except <- "" } } while (!is_null(cnd)) { if (inherits(cnd, "error")) { out <- handlers[[1L]](cnd) if (!inherits(out, "rlang_zap")) throw(out) } inherit <- .subset2(.subset2(cnd, "rlang"), "inherit") if (is_false(inherit)) { return() } cnd <- .subset2(cnd, "parent") }})
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(withCallingHandlers(expr, condition = function(cnd) { { .__handler_frame__. <- TRUE .__setup_frame__. <- frame if (inherits(cnd, "message")) { except <- c("warning", "error") } else if (inherits(cnd, "warning")) { except <- "error" } else { except <- "" } } while (!is_null(cnd)) { if (inherits(cnd, "error")) { out <- handlers[[1L]](cnd) if (!inherits(out, "rlang_zap")) throw(out) } inherit <- .subset2(.subset2(cnd, "rlang"), "inherit") if (is_false(inherit)) { return() } cnd <- .subset2(cnd, "parent") }}), stackOverflowError = handlers[[1L]])
7: rlang::try_fetch(rapi_execute(stmt, arrow, integer64), error = function(e) { rethrow_error_from_rapi(e, call)})
8: rethrow_rapi_execute(res@stmt_lst$ref, res@arrow, res@connection@bigint == "integer64")
9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(conn, "LOAD 'httpfs';")
17: DBI::dbExecute(conn, "LOAD 'httpfs';")
18: load_httpfs(conn)
19: parse_uri(sources, conn = conn, recursive = recursive)
20: duckdbfs::open_dataset(urls[tbl])
21: fb_tbl("diet_items")
22: rfishbase::diet_items()
23: as.data.frame(rfishbase::diet_items())
24: ConvertFishbaseDiet(ExcludeStage = NULL)
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
27: tryCatchList(expr, classes, parentenv, handlers)
28: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
29: try(ConvertFishbaseDiet(ExcludeStage = NULL), silent = TRUE)
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
36: doTryCatch(return(expr), name, parentenv, handler)
37: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
38: tryCatchList(expr, classes, parentenv, handlers)
39: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
40: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
41: test_that("ConvertFishbaseDiet function works", { all.diets <- try(ConvertFishbaseDiet(ExcludeStage = NULL), silent = TRUE) if ("try-error" %in% class(all.diets)) { skip("could not connect to remote database") } else { filtered.diets <- ConvertFishbaseDiet(ExcludeStage = "larvae") expect_true(nrow(filtered.diets$DietItems) < nrow(all.diets$DietItems)) expect_length(filtered.diets, 2) expect_equal(ncol(filtered.diets$Taxonomy), 2) }})
42: eval(code, test_env)
43: eval(code, test_env)
44: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
45: doTryCatch(return(expr), name, parentenv, handler)
46: tryCatchOne(expr, names, parentenv, handlers[[1L]])
47: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
48: doTryCatch(return(expr), name, parentenv, handler)
49: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
50: tryCatchList(expr, classes, parentenv, handlers)
51: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
52: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
53: source_file(path, env = env(env), desc = desc, error_call = error_call)
54: FUN(X[[i]], ...)
55: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
56: doTryCatch(return(expr), name, parentenv, handler)
57: tryCatchOne(expr, names, parentenv, handlers[[1L]])
58: tryCatchList(expr, classes, parentenv, handlers)
59: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
60: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
61: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
62: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
63: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
64: test_check("dietr")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang